The discovery of comammox broadens our understanding of the nitrification process, but little is known about its natural geographical distribution and its contribution to nitrogen conversion process. In this study, the surface soils of the paddy fields with different reclamation years (0, 27, 51 and 86 a) were selected in the Chongming wetland of the Yangtze River estuary, soil nitrification rates and its influencing factors were determined by aerobic incubation, and the target functional gene amoA was analyzed by real-time fluorescent quantitative PCR to analyze the quantitative variation characteristics of Comammox, ammoxidox bacteria (AOB) and ammonia archaea (AOA). The results showed that the net nitrification rates of paddy soils with 40, 75 and 120 a of reclamation were N 19.26, 11.63 and 11.43 mg/(kg?d), respectively, which were significantly 5.1-8.7 times higher than that of natural tidal wetland (P<0.05). The amoA gene copy number of soil ammonia archaea AOA was between 0.34×10⁷ and 9.95×10⁷ copies/g, which increased significantly with the increase of reclamation year. The amoA gene copy number of soil ammonia bacteria AOB ranged from 1.14×10⁷ to 8.43×10⁷ copies/g, which was significantly positively correlated with soil nitrification rate (r= 0.96*, P<0.05), indicating that AOB might play a dominated role in nitrification process. The Comammox Clade A and Clade B copy number of the soils in the paddy fields (27, 51 and 86 a) were lower than that of tidal flat wetland soil (no reclamation), and Clade A increased significantly with the increase of the reclamation year. Comammox Clade A/Clade B was significantly negatively correlated with soil total organic carbon (TOC) and ammonium content (NH₄⁺), indicating that the ammonia-oxidizing microbes (Clade A, Clade B) are more suitable for nutritional infertility. In summary, Comammox bacteria is widely present in the coastal wetland soils of the Yangtze River estuary, which possibly may play an important role in nitrogen transformation process of tidal flat natural wetlands.